Not sure what you're alluding to about Hayate and Hina being in the old school building, and what that has to do with Nagi.
As for people being able to see the Father, didn't he say anyone who was there when the church was destroyed could see him? That would basically imply Hayate, Nagi, Hina, Sakuya, Isumi, Wataru, the Sister, and Yukiji can see him.
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